Contacts of the helix formed by residues 400 - 412 (chain A) in PDB entry 3THY
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 400 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A LYS* 5.9 1.2 - - - +
399A ALA* 1.3 75.6 - - - +
401A LEU* 1.3 67.5 + - - +
402A GLN* 2.9 40.2 + - - +
403A ASP* 3.0 36.6 + - - +
404A CYS* 3.4 9.4 + - - -
406A ARG* 5.3 0.6 - - - +
578A VAL* 5.3 4.0 - - + -
582A VAL* 4.6 5.6 - - - -
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Residues in contact with LEU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A ASN* 1.3 75.6 - - - +
402A GLN* 1.3 63.3 + - - +
404A CYS* 3.1 20.7 + - + +
405A TYR* 3.1 11.4 + - - +
457A THR* 5.8 1.8 - - - +
458A LEU* 3.6 31.2 - - + +
468A PHE* 3.2 38.1 - - + +
469A LEU* 4.0 14.8 - - - -
470A VAL* 4.4 11.9 - - + +
578A VAL* 4.5 30.5 - - + +
581A ILE* 4.8 22.4 - - + -
582A VAL* 5.9 0.7 - - + -
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASN* 2.9 15.4 + - - +
401A LEU* 1.3 78.0 - - - +
403A ASP* 1.3 61.0 + - - +
405A TYR* 3.1 3.5 + - + +
406A ARG* 3.0 53.2 + - + +
466A HIS* 4.9 10.4 - - - -
468A PHE* 3.1 54.0 - - + -
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Residues in contact with ASP 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390A LEU* 4.0 16.0 - - + +
393A LYS* 3.2 22.2 + - - +
394A PHE* 4.1 6.0 - - + -
398A ALA 4.4 0.2 - - - +
399A ALA* 3.2 19.6 - - + -
400A ASN* 3.0 44.6 + - - +
402A GLN* 1.3 77.2 - - - +
404A CYS* 1.3 61.7 + - - +
406A ARG* 2.7 40.7 + - - +
407A LEU* 3.0 22.5 + - - +
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Residues in contact with CYS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394A PHE* 3.8 27.8 - - - -
400A ASN 3.4 9.2 + - - -
401A LEU* 3.1 16.7 + - + +
403A ASP* 1.3 79.0 - - - +
405A TYR* 1.3 51.5 - - - +
407A LEU* 3.4 4.8 + - - +
408A TYR* 2.7 34.4 + - - +
450A PHE* 3.8 7.1 - - + -
454A ILE* 4.1 19.9 - - + +
458A LEU* 5.2 0.7 - - + -
581A ILE* 4.7 11.7 - - - -
582A VAL* 4.3 13.7 - - - -
585A SER* 4.0 16.2 - - - -
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Residues in contact with TYR 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A LEU 3.1 9.6 + - - +
402A GLN* 3.1 14.2 + - + +
404A CYS* 1.3 75.1 - - - +
406A ARG* 1.3 61.7 + - + +
408A TYR* 3.2 15.6 - + + +
409A GLN* 2.6 81.3 + - + +
454A ILE* 5.2 1.3 - - + -
458A LEU* 3.8 28.2 - - + +
460A MET* 4.9 10.1 - - - -
463A VAL* 3.7 28.0 - - + +
464A GLU* 5.7 0.3 + - - -
468A PHE* 4.1 18.6 - + + -
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A PRO* 3.9 19.6 - - + +
390A LEU* 4.5 18.8 - - + +
393A LYS* 4.5 16.6 - - - +
400A ASN* 5.3 0.8 - - - +
402A GLN* 3.0 52.0 + - + +
403A ASP* 2.7 35.5 + - - +
405A TYR* 1.3 80.0 - - + +
407A LEU* 1.3 61.3 + - - +
409A GLN* 3.7 8.7 - - - +
410A GLY 3.1 16.8 + - - -
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Residues in contact with LEU 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385A PRO* 5.0 1.8 - - - -
387A LEU* 4.6 12.8 - - + -
390A LEU* 3.5 18.7 - - + +
394A PHE* 3.5 25.8 - - + -
403A ASP 3.0 11.1 + - - +
404A CYS* 3.5 7.6 - - - +
406A ARG* 1.3 73.4 - - - +
408A TYR* 1.3 64.7 + - - +
410A GLY* 3.2 2.6 + - - -
411A ILE* 3.0 42.1 + - + +
447A PHE* 4.8 7.2 - - + -
450A PHE* 3.5 31.6 - - + -
585A SER* 5.4 1.3 - - - -
588A TYR* 5.6 2.0 - - + -
592A MET* 3.6 24.9 - - + -
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Residues in contact with TYR 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A CYS 2.7 18.6 + - - +
405A TYR* 3.2 20.6 - + - +
407A LEU* 1.3 70.3 - - - +
409A GLN* 1.3 87.2 + - - +
411A ILE 3.0 13.5 + - - -
412A ASN* 3.0 32.2 + - - +
450A PHE* 4.2 2.5 - + + -
451A GLN* 3.4 56.1 - - + +
454A ILE* 3.9 23.6 - - + -
455A GLU* 3.0 39.1 + - + +
460A MET* 4.7 12.9 - - + +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A ARG 5.1 2.9 - - - +
405A TYR* 2.6 73.1 + - + +
406A ARG* 3.7 8.3 - - - +
408A TYR* 1.3 88.5 - - - +
410A GLY* 1.3 65.5 + - - +
412A ASN* 3.3 16.4 + - - +
413A GLN* 3.8 13.9 + - - +
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Residues in contact with GLY 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A ARG 4.2 8.0 + - - -
384A PHE* 3.4 16.1 - - - -
385A PRO* 4.2 19.9 - - - +
387A LEU* 6.2 1.3 - - - -
406A ARG 3.1 10.5 + - - -
407A LEU* 3.6 4.5 - - - -
408A TYR 3.0 1.0 - - - -
409A GLN* 1.3 78.8 - - - +
411A ILE* 1.3 57.7 + - - +
412A ASN 3.0 0.2 - - - -
413A GLN* 2.8 28.9 + - - +
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Residues in contact with ILE 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A PHE* 5.1 2.0 - - - -
387A LEU* 6.3 0.4 - - + -
407A LEU* 3.0 29.7 + - + +
408A TYR 3.0 4.8 + - - -
410A GLY* 1.3 69.6 - - - +
412A ASN* 1.3 57.8 + - - +
413A GLN 3.1 2.7 + - - -
414A LEU* 3.4 22.2 - - + +
415A PRO* 3.6 4.2 - - - +
444A ARG* 3.7 17.5 + - - +
447A PHE* 3.1 54.3 - - + -
450A PHE* 4.4 0.7 - - + -
451A GLN* 3.3 43.1 - - + +
595A LEU* 4.8 11.7 - - + -
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Residues in contact with ASN 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A TYR* 3.0 35.9 + - + +
409A GLN* 3.6 15.9 - - - +
410A GLY 2.9 1.6 + - - -
411A ILE* 1.3 78.3 - - - +
413A GLN* 1.3 66.8 + - + +
414A LEU 3.5 0.2 - - - -
415A PRO* 3.6 16.2 - - - +
416A ASN* 4.8 2.9 + - - -
444A ARG* 5.3 3.8 + - - +
451A GLN* 3.5 12.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il